title: Bulk RNA-seq of Early Time Course Colonic Epithelia from Satb2-deficient and WT mice

city: Shanghai

first: Wei

last: Gu

address: 51 Rijing Road

department: Beigene Institute

institute: Beigene

summary: Given that SATB2 is expressed in differentiated colonic cells as well as the stem cells, we evaluated whether SATB2 might directly regulate the identity of the differentiated cells

overall_design:
We administered a single dose of tamoxifen (TAM) to Satb2cKO or control mice and examined transcriptal expression level at 1, 2, 4, or 6 days after TAM
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

first: Judith

last: Kraiczy

first: Xiaofeng

last: Huang

first: Ramesh

last: Shivdasani

first: Qiao

last: zhou


title: Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster [ChIPmentation]

status: Public on Oct 05 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIPmentation-seq analysis of CTCF and RAD21 in wildtype and mutant CTCF binding sites alleles

first: Ana

middle: R

last: Amândio

first: Leonardo

last: Beccari

first: Bénédicte

last: Mascrez

first: Jozsef

last: Zakany

first: Sandra

last: Gitto

first: Denis

last: Duboule


title: Bulk RNA-seq of Colonic Epithelia from EED and EED/Satb2 Double Knockout Mice

state: Shanghai

country: China

type: Expression profiling by high throughput sequencing

summary: To understand the polycomb repressive complex 2 (PRC2) function, we genetically deleted EED, which inactivated PRC2, in adult intestine and colon using (VillinCreER-T2;EEDf/f).

overall_design:
Conditional knockout EED in wild type and Satb2cKO adult intestine.
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

middle: A


title: The role of m6A methylation modification in CPB2 toxin treatment of porcine small intestinal epithelial cells

city: Lanzhou

first: Zhang

middle: Juan

last: li

address: No. 1 Yingmen Village

institute: Gansu Agricultural University

summary: In this experiment, m6A-seq sequencing technology was used to study the functional role of methylated molecules in the process of CPB2 processing porcine small intestinal epithelial cells. In this experiment, an IP library and an input library were built together. The IP library was enriched with m6A specific antibodies to generate methylated RNA, and the influence of m6A methylation modification on its expression was analyzed by bioinformatics. We finally concluded that m6A methylation modification may play a very important role after CPB2 toxin treats small intestinal epithelial cells.

overall_design: Take the blank treatment as the control, and treat the porcine small intestinal epithelial cells with 20ug/ml CPB2 as the CPB2 group. The two groups simultaneously treat the small intestinal epithelial cells for 24h


title: Bulk RNA-seq of Epitope Expressed SATB2 in Mouse Ileum Epithelium

summary: To investigate if Satb2 is sufficient to confer colonic fate from the small intestine mucosa, we generated a transgenic mouse  line, CAGSATB2-GFP, in which CRE excision of a stop cassette activates HA epitope-tagged  SATB2 and GFP fluorescence.

overall_design:
FACS sorting out GFP+ (SATB2OE) and GFP- (Ctrl) cells from ileum epithelium.
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

last: Zhou


title: Bulk RNA-seq of Mouse Colonic Organoids: SATB2 and FOXD2KO CRISPR Knockout

summary: CRISPR knock out the Satb2 or Foxd2 gene from mouse colonic organoids to validate core human and mouse large intestine stem cell enrich TFs.

overall_design:
Three genomic modified mouse colonic organoids (Ctrl, Foxd2 and Satb2 sgRNAs) were differentiated and collected for Bulk RNA-Seq
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.


title: Bulk RNA-seq of 3D Cultured Intestinal Organoids (Ileum and Colon) from Satb2-deficient and WT mice

summary: The colonic microenvironment may have influenced gene expression of the ileal-like mucosa in Satb2KO colon In Vivo. We use 3D culture organoid system In Vitro to mitigate the environmental influence.

overall_design:
All organoids were estimated in lagre intestine culture medium and passaged one generation. The differentiated organoids were collected for Bulk RNA-Seq
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.


title: Identification of EMT and EMT/Cilium-dependent gene expression signatures + Identification of breast tumors of the claudin-low molecular subtype among triple-negative breast cancers

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

summary: The goal of the first gene expression analysis reported here (Samples 1-16) was to establish gene expression signatures associated to activation of an Epithelial-Mesenchymal Transition (EMT) and primary ciliogenesis, in immortalized and non-transformed (HMLE) or transformed (HMLER) human mammary epithelial cells, respectively. The goal of the second gene expression analysis (Samples 17-83) was to determine the molecular subtypes of human breast cancers of a triple-negative breast cancer (TNBC) biobank.

overall_design:
Samples 1-16: Epithelial-like (shCTL, CTL) and Mesenchymal-like (shEcad, Snail) HMLE and HMLER cells non-treated or treated with DMSO or Ciliobrevin A were analyzed.
Samples 17-83: Triple-negative breast tumors (17-78) and control luminal breast tumors (79-83) were analyzed.

first: Vincent

middle: J

last: Guen

first: Molly

middle: M

last: Wilson

first: Matthieu

last: Le Gallo

first: Jacqueline

last: Lees


title: Gene expression analysis of yeast lacking Set4 under normal and stress conditions

city: Baltimore

first: Erin

last: Green

state: MD

address: 1000 Hilltop Cir, Bs 325

department: Biological Sciences

institute: UMBC

summary: Genome-wide gene expression data were generated for wildtype and set4 mutant yeast under aerobic and hypoxic conditions to determine the contribution of Set4 to gene expression. Illumina-based sequencing was performed on strand-specific libraries prepared from mRNA purified from yeast grown in rich medium aerobically or under hypoxia. Reads were processed for qualiy control, mapped to the genome, and differential gene expression was determined based on log fold-change differences between set4 mutants and wildtype.

overall_design: Three replicates each of wildtype and set4 mutant yeast grown in YPD medium, 30 degrees C either under aerobic or hypxic conditions are reported

first: Yogita

last: Jethmalani

first: Khoa

last: Tran

first: Mark

last: Ramos

first: Eric

last: Garcia

first: Maki

last: Negesse

first: DoHwan

last: Park


title: Bulk RNA-seq of CRISPR SATB2 Knockout Human Colonic Organoids

first: Wei

last: Gu

summary: To evaluate SATB2 function in human colonic epithelium, we knocked out the SATB2 gene in 3D cultured human colonic organoid.

overall_design:
Colonic organoids cultured from 5 different donors were knocked out the SATB2 gene by CRISPR. Organoids were differentiated for 3 days before RNA was collected.
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

first: Xiaofeng

last: Huang

first: Qiao


title: Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: While critical for host defense, innate immune cells are also pathologic drivers of acute respiratory distress syndrome (ARDS). Innate immune dynamics during COVID-19 ARDS, compared to ARDS from other respiratory pathogens, is unclear. Moreover, mechanisms underlying beneficial effects of dexamethasone during severe COVID-19 remain elusive. Using scRNA-seq and plasma proteomics, we discovered that compared to bacterial ARDS, COVID-19 was associated with expansion of distinct neutrophil states characterized by interferon (IFN) and prostaglandin (PG) signalling. Dexamethasone during severe COVID-19 depleted circulating neutrophils, altered IFNactive neutrophils, downregulated interferon-stimulated gene, and activated IL1R2+ve neutrophils. Dexamethasone also expanded immunosuppressive immature neutrophils and remodeled cellular interactions by changing neutrophils from information receivers into information providers. Male patients had higher proportions of IFNactive neutrophils, preferential steroid-induced immature neutrophil expansion, and possibly different effects on outcome. Our single-cell atlas (www.biernaskielab.ca/COVID_neutrophil) defines COVID-19-enriched neutrophil states and molecular mechanisms of dexamethasone action to develop targeted immunotherapies for severe COVID-19.

overall_design:
Leukocyte and lymphocyte preparation:

For lymphocyte preparation, whole blood (2mL) was collected in 5mL polystyrene round-bottom tubes. Tubes were spun (15min, 3000rpm, Room Temperature [RT]) and plasma was removed. 100 microL of Isolation Cocktail and 100 microL of Rapid Spheres (Easy SepTM Direct Human Total Lymphocytes Isolation Kit: 19655, StemCell Technologies) were added to the remaining whole blood. After mixing and 5min incubation at RT, the sample volumes of ≤ 2.5mL blood were topped up to 5mL with D-PBS+2%FBS + 1mM EDTA. The diluted sample was incubated in the magnet without lid for 5min, at RT. This last step was repeated twice before cell resuspension in 5mL of PBS+0.04% BSA. After 2 washes in PBS+0.04% BSA, and centrifugation for 5 min at 2000rpm, 7500 lymphocytes were resuspended in 25 microL of PBS+0.04% BSA.

For leukocytes preparation, whole blood was collected in heparin containing vacutubes and 12 microL of 0.5M EDTA with 1mL of PBS+2% FBS and 50 microL of RBC of EasySep RBC Depletion spheres (EasySepTM RBC Depletion Reagent: 18170, Stem Cell Technologies) were added. After 5 min of magnet incubation, at RT, tubes were inverted and poured into a new tube. 50 microL of RBC depletion spheres were added. 5 min after incubation on the magnet, the tube was inverted, and cell suspension was poured into a new 15mL tube. After 2 washes in 5mL of PBS+0.04% BSA and centrifugation at 2000rpm for 5 min at 20oC, cells were resuspended in 25 microL of PBS+0.04% BSA.

Single-cell RNA-Seq library construction, alignment, and quality control:

A total of 15,000 single cells (containing an equal proportion of leukocytes and lymphocytes) were loaded for partitioning using 10X Genomics NextGEM Gel Bead emulsions. All samples were processed as per manufacturer’s protocol. Quality control and pre-loading cDNA quantification was performed using TapeStation D1000 ScreenTape assay. Sequencing was performed using Illumina NovaSeq S2 and SP 100 cycle dual lane flow cells over multiple rounds to ensure each sample received approximately 32,000 reads per cell. Sequencing reads were aligned using CellRanger 3.1.0 pipeline29 to two sets of reference genomes: 1. standard pre-built GRCh38 human reference, and 2. a modified GRCh38 reference with two SARS-CoV-2 genomes (MT412228 and MN908947.3) appended. Since no SARS-CoV-2 reads were detected in whole blood single-cell samples30, all analyses presented in this manuscript were performed using standard pre-built GRCh38 reference. Samples that passed alignment QC were aggregated into single datasets using CellRanger aggr with between-sample normalization to ensure each sample received an equal number of mapped reads per cell. Aggregated non-dexamethasone-treated COVID-19 (n = 12) and bacterial ARDS (n = 9) samples recovered 1,872,659 cells that were sequenced to 38,410 post-normalization reads per cell. Likewise, aggregated COVID-19 samples with (n = 9) or without (n = 12) dexamethasone recovered 1,748,551 single cells sequenced to 51,415 post-normalization reads per cell.

Processed data availability:

Single-cell datasets can be further explored on our companion portal at http://biernaskielab.ca/COVID_neutrophil or http://biernaskielab.com/COVID_neutrophil. Velocyto-generated LOOM files and processed R objects are available for reanalysis from: http://doi.org/10.6084/m9.figshare.14330795. Whole blood bulk RNA-Seq datasets employed as an independent validation cohort were downloaded from GSE157103. BALF scRNA-Seq datasets from severe and moderate COVID-19 were downloaded from GSE145926. Processed BALF scRNA-Seq objects from patients with bacterial pneumonia and COVID-19 (archived at GSE167118) were downloaded from authors’ archive: https://figshare.com/articles/dataset/_/13608734. Mass spectrometry datasets are available via ProteomeXchange Consortium via the PRIDE partner repository with identifier PXD028429.

first: Sarthak

last: Sinha

first: Nicole

middle: L

last: Rosin

first: Rohit

last: Arora

first: Elodie

last: Labit

first: Arzina

last: Jaffer

first: Leslie

last: Cao

first: Raquel

last: Farias

first: Angela

middle: P

last: Nguyen

first: Luiz

middle: G

last: N de Almeida

first: Antoine

last: Dufour

first: Amy

last: Bromley

first: Braedon

last: McDonald

last: Gillrie

first: Marvin

last: Fritzler

first: Bryan

last: Yipp


title: Bulk RNA-seq of Intestine Epithelia (Jejunum, Ileum, Cecum and Colon) from Satb2-deficient and WT mice

first: Wei

last: Gu

summary: The goal of this study is to study the consequence of Satb2 gene loss in the colonic epithelium.

overall_design:
Intestine epithelium isolated from adult mice. Genotypes include Vil-CreER;SATB2F/F (SATB2KO) and Satb2f/f (Wild Type)
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

first: Xiaofeng

last: Huang

last: Zhou


title: Correlation of clinical parameters of heart failure with myocardial gene expression in dilated cardiomyopathy

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

summary: To gain new insights into the complex pathophysiology of dilated cardiomyopathy (DCM) we performed a quantitative approach to identify genes with expression patterns that linearly correlate with parameters of cardiac morphology (left ventricular end-diastolic diameter indexed by body surface are (LVEDDI), systolic function (LV ejection fraction (LVEF)), and serum levels of cardiac peptide hormone N-terminal pro-brain natriuretic peptide (NT-proBNP) in human endomyocardial biopsies of 47 DCM patients and 8 individuals with normal LVEF. A set of genes was identified as common heart failure markers characterized by correlation of their expression with cardiac morphology, systolic function and NT-proBNP. Among them are already known genes encoding e.g. the natriuretic peptide hormones NPPA and NPPB and its converting enzyme corin, but also potential new HF markers like EP300 antisense RNA1 and dimethylarginine dimethylaminohydrolase 1 (DDAH1) along with other genes with so far unknown relation to heart function. In contrast, the expression of other genes including the Ca2+ flux regulating genes phospholamban (PLN), sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA), and extracellular matrix proteins showed significant correlation with LVEF and LVEDDI only. Those genes seem to reflect more specifically pathological alterations of systolic function and morphology in DCM hearts.

overall_design: This study comprises 47 DCM patients with LV systolic dysfunction (LVEF <45%) and symptoms of HF according to the New York Heart Association (NYHA) functional class II and III . Data from a subset of these patients had been reported in regard to their response on an intervention previously (Ameling et al, 2013). Transcriptome analyses were performed from endomyocardial biopsies which were no longer needed for routine diagnostics. Written informed consent was obtained by each patient and the protocol was approved by the Ethics Committee of the University of Greifswald, Germany and to the principles of the Declaration of Helsinki.

first: Eric

last: Witt

first: Elke

last: Hammer

first: Marcus

last: Dörr

first: Kerstin

last: Weitmann

first: Daniel

last: Beug

first: Matthias

last: Nauck

first: Uwe

last: Völker

first: Stephan

middle: B

last: Felix


title: Mouse papillomavirus methylation signature is characterized by hypermethylation and retention of viral memory after lesion regression

status: Public on Oct 12 2021

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: We sought to describe the global methylation landscape of mouse papillomavirus (MmuPV1) in the context of active and regressed MmuPV1 lesion tissue

overall_design: Mice that were immune-suppressed using the drug Cyclosporin (CsA) were infected with MmuPV1 on their tails. Wart lesions developed and the skin of these lesions was harvested (Active group), or allowed to heal by withdrawing CsA and then harvested (Regressed group). Reduced Representation Bisulphite Sequencing (RRBS) was used to compare methylation patterns between the groups and their controls

first: Allison

last: Tschirley

first: Peter

last: Stockwell

first: Euan

last: Rodger

first: Neil

last: Christensen

first: Ian

last: Morrison

first: Merilyn

last: Hibma


title: Identification of EMT and EMT/Cilium-dependent gene expression signatures + Identification of breast tumors of the claudin-low molecular subtype among triple-negative breast cancers II

first: Charles

last: Whittaker

summary: The goal of the second gene expression analysis (samples 17-83) was to determine the molecular subtypes of human breast cancers of a triple-negative breast cancer (TNBC) biobank.

overall_design: Triple-negative breast tumors (17-78) and control luminal breast tumors (79-83) were analyzed

first: Vincent

last: Guen

first: Molly

last: Wilson

first: Matthieu

last: Le Gallo

first: Jacqueline

last: Lees


status: Public on Oct 04 2021

city: Boston

first: Lynn

last: Bry

address: 75 Francis St.

institute: Brigham and Women's Hospital

summary: We illustrate how metabolically distinct species of Clostridia can protect against or worsen Clostridioides difficile infection, modulating the pathogen's colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Paraclostridium bifermentans survived infection while mice colonized with the butyrate-producer, Clostridium sardiniense, more rapidly succumbed. Systematic in vivo analyses revealed how each commensal altered the gut nutrient environment, modulating the pathogen's metabolism, regulatory networks, and toxin production. Oral administration of P. bifermentans rescued conventional mice from lethal C. difficile infection via mechanisms identified in specifically colonized mice. Our findings lay the foundation for mechanistically informed therapies to counter C. difficile disease using systems biologic approaches to define host-commensal-pathogen interactions in vivo.

overall_design:
(i)  Gnotobiotic mice were colonized with Paracolostridium bifermentans ATCC 638 or Clostridium sardiniense DSM 599 7 days prior to infection with 10^3 spores of Clostridioides difficile ATCC 43255. Cecal contents were collected an analyzed at the indicated timepoints. Compared to mono-associated (MA) infections, mice pre-colonized with P. bifermentans showed significant protection from severe disease, whereas those pre-colonized with C. sardiniense more quickly succumbed.
Additional metabolomic experiments were coupled with these results and suggest that metabolic competition and symbiosis, respectivevly, in the gut play a major role in C. difficile disease.
Mice were pre-colonized with a gut commensal bacterial species, then infected with C. difficile.
(ii)  Csar
In vivo commensal control of Clostridioides difficile virulence, Clostridium sardiniense transcriptome:
Gnotobiotic mice were colonized with Clostridium sardiniense DSM 599 7 days prior to infection with 10^3 spores of Clostridioides difficile ATCC 43255. Cecal contents were collected an analyzed at the indicated timepoints. Compared to mono-associated (MA) infections, mice pre-colonized with P. bifermentans showed significant protection from severe disease, whereas those pre-colonized with C. sardiniense more quickly succumbed.
Additional metabolomic experiments were coupled with these results and suggest that metabolic competition and symbiosis, respectivevly, in the gut play a major role in C. difficile disease.
Mice were pre-colonized with a gut commensal bacterial species, then infected with C. difficile.
(iii)  PBI
In vivo commensal control of Clostridioides difficile virulence, Paraclostridium bifermentans transcriptome:
Gnotobiotic mice were colonized with Paracolostridium bifermentans ATCC 638 7 days prior to infection with 10^3 spores of Clostridioides difficile ATCC 43255. Cecal contents were collected an analyzed at the indicated timepoints. Compared to mono-associated (MA) infections, mice pre-colonized with P. bifermentans showed significant protection from severe disease, whereas those pre-colonized with C. sardiniense more quickly succumbed.
Additional metabolomic experiments were coupled with these results and suggest that metabolic competition and symbiosis, respectivevly, in the gut play a major role in C. difficile disease.

first: Jay

middle: N

last: Worley

first: Brintha

last: Girinathan

first: Nicholas

last: DiBenedetto


title: Single-Cell RNA Sequencing in Multiple Pathologic Types of Renal Cell Carcinoma Revealed Novel Potential Tumor-Specific Markers

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: We provide a comprehensive, single-cell resolution, multiple pathologic transcriptome map of renal cell carcinoma (RCC).A total of 4 tumor samples and 1 normal kidney sample from four patients with renal cell carcinoma participated in this study.We present 30,263 cells (pRCC=10,132, ccRCC=12,915,chRCC=7,216,normal=585) after strictly quality control.scRNA-seq analysis revealed tumor heterogeneity at the single-cell level between different pathological types or between different cell types of the same pathological type. Meanwhile, we discovered a number of novel tumor markers of RCC which will offer potential value in diagnosing this disease. In addition, we identified some new cell types by scRNA-seq, such as proliferative TAM, proliferative fibroblast and novel endothelial cells. The comparative analysis between normal kidney and RCC had enhanced our understanding of tumor-immune microenvironment. Taken together, our data has greatly enriched the single-cell transcriptomic information for RCC, which will provide new insights into the diagnosis and treatment of RCC.

overall_design: Five samples (2 clear cell renal cell carcinoma samples,1 papillary renal cell carcinoma sample,1 chromophobe renal cell carcinoma sample and 1 normal kidney sample) from 4 patients were used for single cell RNA sequencing by 10X Genomics.


title: Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

summary: RNA-seq of cytoplasmic RNAs in RNase L KO A549 cells shows increased intron load compared to WT cells.

overall_design: WT and RNase L KO A549 cells treated with lipofectamine for 12h, cytoplasmic fraction was collected, followed by ribosome depletion and directional RNA-seq.

first: Chitrakar

last: Alisha

first: Solorio

last: Kristina

first: Prangley

last: Eliza

first: Korennykh

last: Alexei


title: An EMT-primary cilium-GLIS2 signaling axis regulates mammogenesis and claudin-low breast tumorigenesis

summary: The Epithelial–Mesenchymal Transition (EMT) and primary ciliogenesis induce stem cell properties in basal Mammary Stem Cells (MaSCs) to promote mammogenesis, but the underlying mechanisms remain incompletely understood. Here, we show that EMT transcription factors promote ciliogenesis upon intermediate EMT transition states by activating ciliogenesis inducers, including FGFR1. The resulting primary cilia promote BBS11-dependent ubiquitination and inactivation of a central signaling node, GLIS2. We show that GLIS2 inactivation promotes MaSC stemness, and GLIS2 is required for normal mammary gland development. Moreover, GLIS2 inactivation is required to induce the proliferative and tumorigenic capacities of the Mammary-Tumor-initiating cells (MaTICs) of claudin-low breast cancers. Claudin-low breast tumors can be segregated from other breast tumor subtypes based on a GLIS2-dependent gene expression signature. Collectively, our findings establish molecular mechanisms by which EMT programs induce ciliogenesis to control MaSC and MaTIC biology, mammary gland development, and claudin-low breast cancer formation.

overall_design: Three replicate of Glis2 KO mammary glands compared to three replicates of WT control mammary glands.

first: Céline

last: Callens

first: Svetlana

last: Mironov

first: Qiong

last: Ding

first: Amandine

last: Salamagnon

first: Roselyne

last: Viel

first: Tony

middle: E

last: Chavarria

first: Abena

middle: D

last: Peasah

first: Arjun

last: Bhutkar

first: Sophie

last: Martin

first: Florence

last: Godey

first: Hong

middle: S

last: Kang

first: Philippe

last: Juin

first: Patrick

last: Tas

first: Anton

last: Jetten

first: Jane

last: Visvader

first: Robert

last: Weinberg

first: Massimo

last: Attanasio

first: Claude

last: Prigent


title: Bulk RNA-seq of Human Duodenal and Colonic Stem Cells

first: Wei

last: Gu

summary: The screening of human large intestine epithelial enriched transcript factors by comparing high WNT condition cultured human duodenal and colonic organoids.

overall_design:
Human duodenal and colonic organoids in high WNT condition from 8 different donors were collect for RNA-seq
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.

first: Xiaofeng

last: Huang

first: Qiao

last: Zhou


title: Bulk RNA-seq (>20M reads) of Intestine Epithelium (Ileum and Colon) from Satb2-deficient and WT mice

summary: Resequening ileum and colon epithelium with deeper reads to evaluate consequence of Satb2 gene loss in the colonic epithelium. The same library construction method was used to compare with Bulk RNA-seq data from In Vitro cultured mouse organoids.

overall_design:
Deep RNA-seqenucing in intestine epithelium (WT Ileum, WT Colon and SATB2KO Colon). Genotypes include Vil-CreER;SATB2F/F (SATB2KO) and Satb2f/f (Wild Type).
Please note that the additional raw counts data (prior to normalization), which was generated from the process of generation of counts relative to genes using featureCounts with default parameters (unstranded mode), was included in the records on Nov 5, 2021.


title: The APC/CFZY-1/Cdc20 complex coordinates with OMA-1 to regulate the oocyte-to-embryo transition in C. elegans

status: Public on Oct 02 2021

city: Wuhan

first: Donglei

last: Zhang

address: 13 Hangkong Rd

department: Biochemistry and Molecular Biology

institute: Huazhong University of Science and Technology

summary: During oocyte maturation and the oocyte-to-embryo transition, key developmental regulators such as RNA-binding proteins coordinate translation of particular mRNAs and related developmental processes by binding to their cognate maternal mRNAs. In the nematode C. elegans, these processes are regulated by a set of CCCH zinc finger proteins. OMA-1 and OMA-2 are two functionally redundant CCCH zinc finger proteins that turnover rapidly during the first embryonic cell division. These turnovers are required for proper transition from oogenesis to embryogenesis. A gain-of-function mutant of OMA-1, oma-1(zu405), stabilizes and delays degradation of OMA-1, resulting in delayed turnover and mis-segregation of other cell fate determinants, which eventually causes embryonic lethality. We performed a large-scale forward genetic screen to identify suppressors of the oma-1(zu405) mutant. We show here that multiple alleles affecting functions of various APC/C subunits, including MAT-1, MAT-2, MAT-3, EMB-30, and FZY-1, suppress the gain-of-function mutant of OMA-1. Mutations in APC/C genes prevent OMA-1 enrichment in P granules and correct delayed degradation of downstream cell fate determinants including PIE-1, POS-1, MEX-3, and MEG-1. Transcriptome analysis also suggested that overall transcription in early embryos occurred after introducing mutations in APC/C genes into the oma-1(zu405) mutant. We demonstrated that only the activator FZY-1, but not FZR-1, is incorporated in the APC/C complex to regulate the oocyte-to-embryo transition. Our findings suggested a genetic relationship linking the APC/C complex and OMA-1, and support a model in which the APC/C complex promotes P granule accumulation and modifies RNA binding of OMA-1 to regulate the oocyte-to-embryo transition process.

overall_design: Examination of transcriptome differences among the oma-1, fzy-1;oma-1, and the wild type.

first: Ying


title: Transcription Factor MEF2D is Required for the Maintenance of MLL-rearranged Acute Myeloid Leukemia

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Early Life Inflammation Primes a Th2-Fibroblast Niche in Skin

status: Public on Oct 01 2021

city: San Francisco

first: Ian

middle: Chen

last: Boothby

state: CA

address: 513 Parnassus Ave, HSW-1201B

institute: University of California San Francisco

summary: Inflammation early in life can prime the local immune milieu of peripheral tissues, causing lasting changes in immunologic tone that confer disease protection or susceptibility. The cellular and molecular mechanisms that incite changes in immune tone in many nonlymphoid tissues remain largely unknown. We find that time-limited neonatal inflammation induced by transient reduction of neonatal regulatory T cells (Tregs) causes a dramatic dysregulation of subcutaneous tissue in murine skin, accompanied by the selective accumulation of Th2 cells within a distinct microanatomic niche. Th2 cells are maintained into adulthood through interactions with a fibroblast population in skin fascia that we refer to as Th2-interacting fascial fibroblasts (TIFFs), which expand in response to Th2 cytokines to form subcutaneous fibrous bands. Activation of the Th2-TIFF niche by neonatal inflammation primes skin for altered reparative responses to wounding. We further identify fibroblasts in healthy human skin expressing the TIFF transcriptional signature and find these cells at high levels in eosinophilic fasciitis, an orphan disease characterized by inflammation and fibrosis of the skin fascia. Taken together, these data define a novel Th2 niche in skin, functionally characterize a disease-associated fibroblast population, and suggest a mechanism of immunologic priming whereby  inflammation early in life creates networks between adaptive immune cells and stromal cells, establishing an immunological set-point in tissues that is maintained throughout life.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell RNAseq of FACS-purified skin stromal cells from mice (P22 control and Treg-depleted) as well as humans (healthy controls and one eosinophilic fasciitis patient).

middle: C

first: Maxime

last: Kinet

first: Devi

last: Boda

first: Elaine

middle: Y

last: Kwan

first: Sean

last: Clancy

first: Jarish

last: Cohen

first: Ireneusz

last: Habrylo

first: Margaret

last: Lowe

first: Mariela

last: Pauli

first: Ashley

last: Yates

first: Jamie

last: Chan

first: Hobart

middle: W

last: Harris

first: Isaac

last: Neuhaus

first: Timothy

middle: H

last: McCalmont

first: Ari

last: Molofsky

first: Michael

last: Rosenblum


title: Transcriptomic profiling of the walnut endopleura during its development

first: Jie

last: Qiu

address: 100 Guilin Road

institute: Shanghai Normal Uiversity

summary: The color of endopleura is one of the most commercially important characteristics of walnut. There exists one major loci on chromosome 9 significantly associated with the color trait. Zooming in on the GWAS peak region, we found a gene JreChr09G12363 homologous to ANR (BAN) located within this region. ANR encodes an anthocyanidin reductase, which functions as a negative regulator of flavonoid biosynthesis and is involved in procyanidin accumulation in the seed. We further examined the transcriptomic profile of this gene in the endopleura, and found that during the development of endopleura, the expression level of JreChr09G12363 (JrANR) showed a continuously increasing trend, and FPKM value could reach up to ~800, providing support for a role of JrANR playing in the endopleura development.

overall_design: Transcriptomic data for walnut endopleura samples were generated in this study. The samples were harvested at 35, 63, 91, 119, 147 days after pollination during the walnut development stage from walnut cultivar ‘Linzaoxiang’ at Chinese Academy of Forestry. At each time point, endopleuras collected from 7 nuts were mixed into one biological replicate, with three replicates at each stage. Total RNA was extracted using the universal total RNA kit (Tiangen, Beijing, China). Transcriptomic sequencing was performed on the NovaSeq 6000 platform at Novogene Company (Beijing, China).

first: Feiyang

last: Ji

first: Ruimin

last: Huang

first: Dong

last: Pei


title: Dihydroartemisinin suppresses the tumorigenesis and cycle progression of colorectal cancer by targeting CDK1/CCNB1/PLK1 signaling

first: Yi

middle: You

last: Cai

address: No. 600 Yishan Road

department: Gastroenterology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: Dihydroartemisinin (DHA), a well-known antimalarial drug, has been widely investigated as its anti-tumor effects in multiple malignancies. However, its effects and regulatory mechanisms in colorectal cancer (CRC) are still unproved. In this study, the in vitro experiments including CCK8, EdU, Transwell, flow cytometry analyses and in vivo tumorigenesis model were conducted to assess the effects of DHA on the bio-behaviors of CRC cells. Additionally, RNA-seq combined with gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses was used to obtain the targets of DHA and these were verified by molecular docking, qRT-PCR and Western blot. As a result, we found that DHA significantly suppressed the proliferation, DNA synthesis and invasive capabilities, and induced cell apoptosis and cell cycle arrest in HCT116, DLD1 and RKO cells in vitro and in vivo.  Further analyses indicated that the targets of DHA were predominantly enriched in cell cycle-associated pathways, including CDK1, CCNB1 and PLK1, and DHA could bind with CDK1/CCNB1 complex and inhibit the activation of CDK1/CCNB1/PLK1 signaling. Moreover, cucurbitacin E, a specific inhibitor of CDK1/CCNB1 axis enhanced the inhibitory effects of DHA on DNA synthesis and colony formation in HCT116 and DLD1 cells. In short, DHA could suppress the tumorigenesis and cycle progression of CRC cells by targeting CDK1/CCNB1/PLK1 signaling.

overall_design: HCT116 cells with 20μM DHA treated and the control HCT116 cells group

first: YouCai

last: Yi

first: Rui

last: Liang

first: XiaoYu

last: Chen

first: HuiNing

last: Fan

first: Ming

first: Jing

last: Zhang

first: JinShui

last: Zhu


title: Penetrating ballistic brain injury produces acute alterations in sleep and circadian-related genes in the rodent cortex: A preliminary study

status: Public on Sep 30 2021

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: We performed transcriptional profiling in an established rodent model of penetrating ballistic brain injury (PBBI) in conjunction with continuous sleep pattern recording of the first 24 hours after injury. 12 adult male Sprague-Daley rats that were randomized to PBBI (n=6) or sham (n=6) groups, animals received a right unilateral frontal PBBI, then were sacrificed after 24 hours of EGG/EMG recording. Brains were harvested, underwent sectioning and cortical tissue samples were stored. RNA were isolated from tissue samples.

overall_design: RNA-seq of rats after 24 hours: sham and penetrating ballistic brain injury. This dataset includes samples from 11 mice (PBBI (n=6), sham (n=5)).

first: Jennifer

last: Blaze

first: Zhaoyu

last: Wang


title: Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [allele-specific analysis]

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.

overall_design: 48 single cells of Mus musculus induced pluripotent stem cells (iPSCs). iPSCs were obtained by reprogramming of mouse embryonic fibroblasts that come from a cross between a female Mus musculus musculus (Mus) containing transgenic X-linked eGFP (X-eGFP) and male Mus musculus castaneus (Cast). Reprogramming was performed by OSKM overexpression by lentiviral vector.


title: PanCancer Immune Nanostring analysis of PBMCs stimulated with Innate-like T-cell agonists

city: Wellington

first: Ellie-May

last: Jarvis

address: Malaghan Institute of Medical Research, PO Box 7060

institute: Malaghan Institute of Medical Reseatch

summary: We aimed to study the function of NKT, MAIT and V[gamma]9V[delta]2 T-cells in a population of people with cancer. To select appropraite immune parameters to study, we wanted to compare and contrast the expression of immune-related genes in human PBMCs following NKT, MAIT and V[gamma]9V[delta]2 T-cell activation. Aim: to compare the expression of immune-related genes in human PBMCs following NKT-cell activation with alpha-galactosylceramide, MAIT-cell activation with 5-amino-6-d-ribitylaminouracil/Methyl glyoxal, and V[gamma]9V[delta]2 T-cell activation with Bromohydrin pyrophosphate (BrHPP).

overall_design: PBMCs from six healthy donors in singleton were cultured with alpha-galactosylceramide (agc), Bromohydrin pyrophosphate (BrHPP), 5-amino-6-d-ribitylaminouracil/Methyl glyoxal (5aru) or media control for 72 hours. RNA was extracted using a commercially available kit and frozen before application to the PanCancer Immune nCounter Assay (NanoString Technologies, Inc.).

first: Robert

last: Weinkove


title: Blast cells surviving acute myeloid leukemia induction therapy are in cycle with a signature of FOXM1 activity

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

summary: Disease relapse remains common following treatment of acute myeloid leukemia (AML) and is due to chemoresistance of leukemia cells with disease repopulating potential. To date, attempts to define the characteristics of in vivo resistant blasts have focused on comparisons between leukemic cells at presentation and relapse. However, further treatment responses are often seen following relapse, suggesting that most blasts remain chemosensitive. Here we characterize in vivo chemoresistant blasts by studying the transcriptional and genetic features of blasts from before and after induction chemotherapy using paired samples from 6 patients with primary refractory AML.

overall_design: Primary human AML were from the Manchester Cancer Research Centre Tissue Biobank (approved by the South Manchester Research Ethics Committee). Their use was authorized by the Tissue Biobank’s scientific sub-committee, with the informed consent of donors. Blasts were flow sorted according to either a CD45low/intCD34+ (n=5) or CD45low/intCD117+ (n=1) immunophenotype. Total RNA was extracted from 10^3-10^5 sorted blasts using QIAshredder spin columns and an RNeasy® Plus Micro kit (Qiagen). Prior to sequencing RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA yield from the sorted populations ranged from 3.5-475ng. To ensure consistency the sample with the lowest yield was used to define the input (3.5ng) for amplification of all samples. Amplification was performed using a SMARTer Stranded Total RNA-Seq Pico input kit (Clontech, Mountain View, CA). Sequencing was performed using a NextSeq desktop sequencing system (Illumina). A single run (400M reads) of 151bp paired-end sequencing produced a mean of 31.4M reads per sample (range 29.3-33.5M).


title: Camptothecin-Induced Replication Stress Affects DNA Replication Profiling by E/L Repli-Seq

city: Tsu

first: Takuya

last: Hayakawa

state: Mie

address: 1577 Kuriyamachiya

department: Bioresources

country: Japan

institute: Mie University

summary: E/L Repli-seq is a powerful tool for detecting cell type-specific replication landscapes in mammalian cells, but its potential to monitor DNA replication under replication stress awaits better understanding. Here, we used E/L Repli-seq to examine the temporal order of DNA replication in human retinal pigment epithelium cells treated with the topoisomerase I inhibitor camptothecin. We found that the replication profiles by E/L Repli-seq exhibits characteristic patterns after replication-stress induction, including the loss of specific initiation zones within individual early replicating timing domains. We also observed global disappearance of the replication timing domain structures in the profiles, which can be explained by checkpoint-dependent suppression of replication initiation. Thus, our results demonstrate the effectiveness of E/L Repli-seq at identifying cells with replication-stress-induced altered DNA replication programs.

overall_design: Analysis of early and late replicating chromosomal regions in human RPE cells with and without CPT-induced replication stress.


title: Response and recurrence correlates in patients treated with neoadjuvant anti-PD-1 therapy for resectable oral-cavity squamous cell carcinoma

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

summary: Neoadjuvant PD-1 blockade may be efficacious in patients with high-risk, resectable oral-cavity, head-and-neck cancer. To explore correlates of response patterns to neoadjuvant nivolumab treatment and post-surgical recurrences, we analyzed longitudinal tumor and blood samples in a cohort of 12 patients displaying 33% responsiveness. Pretreatment tumor-based detection of FLT4 mutations and PTEN signature enrichment favors response, and high tumor mutational burden improves recurrence-free survival. In contrast, preexisting and/or acquired mutations (in CDKN2A, YAP1, JAK2) correlate with innate resistance and/or tumor recurrence. Immunologically, tumor response after therapy entails T-cell receptor repertoire diversification in peripheral blood and intratumoral expansion of preexisting T-cell clones. A high ratio of regulatory to Th17 T cells in pretreatment blood predicts innate resistance, low cytolytic T-cell signature in pretreatment tumor, and low T-cell receptor repertoire diversity in pretreatment blood. Our study provides a molecular framework to advance neoadjuvant anti-PD-1 therapy for patients with resectable head-and-neck cancer.

overall_design: This dataset contains the RNA-seq of human resectable oral-cavity, head-and-neck tumors

first: Hannah

last: Knochelmann

first: Shirley

last: Lomeli

first: Aayoung

last: Hong

first: Mary

last: Richardson

first: Zhentao

last: Yang

first: Raymond

last: Lim

first: Yan

first: Camelia

last: Dumitras

first: Cynthia

last: Timmers

first: Martin

last: Romeo

first: Carsten

last: Krieg

first: Elizabeth

last: O’Quinn

first: Joshua

last: Horton

first: Steve

last: Dubinett

first: Chrystal

last: Paulos

first: David

last: Neskey

first: Roger

last: Lo


title: Repression precedes independent evolutionary gains of a highly specific gene expression pattern

city: Honolulu

first: Joanne

last: Yew

state: HI

address: 1993 East West Rd

department: PBRC

institute: Univ. of Hawaii at Manoa

summary: This study addresses how activator and repressor sequences evolve and interact during enhancer evolutiom in the context of a fatty acyl-CoA elongase gene that contributes to pheromone production in Drosophila. The highly specific tissue expression of the gene in the ejaculatory bulb resulted from the initial evolution of a repressor sequence prior to the independent evolution of an activator sequence.

overall_design: Transcriptomic profiles were obtained from  8-day old D. melanogaster male ejaculatory bulbs.

first: Jacqueline

last: Chin


title: Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [smart-seq]

first: Vincent

last: Pasque

summary: X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency  binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.

overall_design: single-cell RNA-seq using smart-seq protocol

first: Irene

last: Talon

first: Adrian

last: Janiszewski

first: Bart

last: Theeuwes

first: Thomas

last: Lefevre

first: Juan

last: Song

first: Greet

last: Bervoets

first: Lotte

last: Vanheer

first: Natalie

last: De Geest

first: Suresh

last: Poovathingal

first: Ryan

last: Allsop

first: Jean-Christophe

last: Marine

first: Florian

last: Rambow

first: Thierry

last: Voet


title: Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [ATAC-seq]

overall_design: ATAC-seq


title: Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation


title: Gut microbiota-derived short-chain fatty acids protect against the progression of endometriosis

status: Public on Sep 29 2021

city: Saint Louis

first: Ramakrishna

last: Kommagani

state: MO

address: 425 S. Euclid Ave

department: OB/GYN

institute: Washington university School of Medicine in St. Louis.

summary:
The goal of this study is to compare transcriptome profiling of n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) by RNA-sequencing
Methods: The mRNA profiles of vehicle and n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) were generated by deep sequencing, in triplicate using Illumina NovaSeq-6000 sequencers with 2×150 paired-end reads. Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. qRT–PCR validation was performed using TaqMan assays.
Results: Using a 2.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.01 threshold for inclusion, we identified 1,830 differentially expressed genes (DEGs) between Vehicle and n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc).
Conclusions: Our study represents the first detailed analysis of n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Transcriptome profiling of Vehicle and n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc)

first: Sangappa

last: Chadchan

first: Pooja

last: Popli

first: Eric

last: Tycksen


title: Expression data from PrimeView human gene expression array

city: Chongqing

first: Fenghua

last: Xu

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing

institute: Army Medical Center of PLA

summary:
Gene expression in HCT-116 cells infected with shCtrl and shRFWD3 was detected with a PrimeView human gene expression array.
We performed Affymetrix Human Gene Chip Prime View analysis on  shCtrl and shRFWD3 HCT 116 cells. Of the 1305 differentially expressed genes (DEGs) found in shRFWD3 and shCtrl HCT 116 cells, 629 were up-regulated and 676 were down-regulated based on the threshold of absolute fold change ≥ 2 and FDR < 0.05

overall_design: The total RNA of HCT-116 cells infected with shCtrl and shRFWD3 was extracted. The RNA sequencing was performed with Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000. The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR (|Fold Change| ≥ 2 and FDR < 0.05 as significant).

first: Dongfeng

last: Chen


title: p38 MAP kinase signaling in microglia plays a sex-specific protective role in CNS autoimmunity and regulates microglial transcriptional states [female]

city: Burlington

first: Alyssa

last: Richman

state: VT

address: 106 Carrigan Dr, Rowell Building Rm302

department: Department of Biomedical and Health Sciences

institute: University of Vermont

summary: Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system, representing the leading cause of non-traumatic neurologic disease in young adults. This disease is three times more common in women, yet more severe in men, but the mechanisms underlying these sex differences remain largely unknown. MS is initiated by autoreactive T helper cells, but CNS-resident and CNS-infiltrating myeloid cells are the key proximal effector cells regulating disease pathology. We have previously shown that genetic ablation of p38α MAP kinase broadly in the myeloid lineage is protective in the autoimmune model of MS, experimental autoimmune encephalomyelitis (EAE), but only in females, and not males. To precisely define the mechanisms responsible, we used multiple genetic approaches and bone marrow chimeras to ablate p38α in microglial cells, peripheral myeloid cells, or both. Deletion of p38α in both cell types recapitulated the previous sex difference, with reduced EAE severity in females. Unexpectedly, deletion of p38α in the periphery was protective in both sexes. In contrast, deletion of p38α in microglia exacerbated EAE in males only, revealing opposing roles of p38α in microglia vs. periphery. Bulk transcriptional profiling revealed that p38α regulated the expression of distinct gene modules in male vs. female microglia. Single-cell transcriptional analysis of WT and p38α-deficient microglia isolated from the inflamed CNS revealed a diversity of complex microglial states, connected by distinct convergent transcriptional trajectories. Microglial p38α deficiency in males resulted in enhanced transition from homeostatic to disease-associated microglial states, with the downregulation of regulatory genes such as Atf3, Rgs1, Socs3, and Btg2, and increased expression of inflammatory genes such as Cd74, Trem2, and MHC class I and II genes. The effect of p38α deficiency was divergent in female microglia, with an upregulation of a small subset of inflammatory genes that overlapped with males, but mostly a unique transcriptional profile that also included an upregulation of potentially tissue reparative genes. Taken together, these results reveal the presence of a p38α-dependent sex-specific molecular pathway in microglia that is protective in CNS autoimmunity in males, suggesting that autoimmunity in males and females is driven by distinct cellular and molecular pathways, thus informing the design of novel future sex-specific therapeutic approaches.

overall_design: Microglia with conditional p38 knock out in female and male mice after induction of experimental autoimmune encephalitis were used for single cell RNA sequencing using 10X genomics and cell hashing.

first: Mahalia

last: McGill

first: Joe

last: Boyd

first: Seth

last: Frietze

first: Dimitry

last: Krementsov


title: p38 MAP kinase signaling in microglia plays a sex-specific protective role in CNS autoimmunity and regulates microglial transcriptional states


title: Microenvironmental IL-6 Inhibits Anti-Cancer Immune Responses Generated by Cytotoxic Chemotherapy

city: Cambridge

first: Daniel

middle: Robert

last: Goulet

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

summary: RNA sequencing of tumor and stroma isolated from the bone marrow of wild-type and IL6 KO C57BL/6J mice

overall_design: Bone marrow was isolated from dissected femur and tibia of WT and IL6KO mice. Bone marrow was depleted of red blood cells, then tumor and stromal cells were isolated by FACS. RNA was extracted  and sequenced to a depth of at least 10 million reads per sample, with a read length of 75 nt. Reads were aligned and quantified by salmon, differentially expressed genes were identified by DESeq.

last: Bent

first: Luis

middle: R

last: Millán-Barea

first: Iris

last: Zhuang

first: Julia

last: Fröse

first: Michael

middle: T

last: Hemann


title: p38 MAP kinase signaling in microglia plays a sex-specific protective role in CNS autoimmunity and regulates microglial transcriptional states [male]

overall_design: Microglia with conditional p38 knock out in female and male mice after induction of experimental autoimmune encephalitis were used for single cell RNA sequencing using 10X genomics.


title: Rattus norvegicus  brain tissue samples: Sham-operated vs. Remote limb postconditioning (PostC) and Sham-operated vs. transient middle cerebral artery occlusion (tMCAO)

city: San Bartolomeo in Galdo

first: Antonio

last: Vinciguerra

state: Benevento

address: via Pasquale Circelli 130

country: Italy

institute: Università Politecnica delle Marche

summary:
Transcriptional profiling of miRNAs from rat brain tissues comparing controls (Sham) with ischemic rats (tMCAO) and neuroprotected rats (RLIP)
Internal normalization: ischemic core vs. periischemic and ANOVA comparison across three experimental conditions: Sham, tMCAO and RLIP

overall_design: Three-conditions experiment, Sham vs. tMCAO-PostC tissue samples. Biological replicates: 3 control, 3 tMCAO, 3 PostC from 9 different rats. One replicate per array.

first: Giuseppe

last: Pignataro


title: Cell-type specific meQTL extends melanoma GWAS annotation beyond eQTL and identifies a melanocyte gene regulatory network

city: Rockville

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

summary: To explore the roles of cell-type specific methylation QTL (meQTL) for melanoma GWAS annotation, we generated DNA methylation data from the same sample set as our previouse eQTL study including 106 primary melanocyte cultures. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 106 primary melanocyte cultures. To be able to identify the DNA methylation probes whose methylation levels are correlated with germline genetic variants including the ones associated with melanoma, meQTL analysis was performed in these 106 primary melanocyte cultures using the same method as we did for eQTL study.

overall_design: Bisulphite converted DNA from the 106 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Jiyeon

last: Choi

first: Kevin

middle: M

last: Brown


title: Expression data from in vitro polarized-pathogenic Th17 system transfected with YY1 shRNA lentivirus

city: fuzhou

first: Jinpiao

last: Lin

state: fujian

address: 20 Chazhong Road, Fuzhou, Fujian, China.

department: The First Affiliated Hospital of Fujian Medical University

institute: Department of Laboratory Medicine,Gene Diagnosis Research Center, the First Affiliated Hospital, Fujian Medical University

summary:
The proportion of pathogenic Th17 (pTh17) cells were significantly higher in RA than that in control individuals and showed a potential relevance with YY1 expression. Increased YY1 expression was observed in pTh17, and the pTh17 differentiation was hampered by YY1 knockdown.
We used microarrays to detail the gene expression changes of pTh17 transfected with YY1 shRNA lentivirus and tried to elucidate the potential mechanisms how YY1 can affect pTh17 cell differentiation in RA.

overall_design: Human naïve CD4+ T cells from peripheral blood mononuclear cells of 3 healthy honors were purified and only a CD4+CD45RA+ cell suspension with a purity ≥ 90% was used for following experiments. Purified naïve CD4+ T cells at 2×105 cells per well were cultured in 96-well round-bottom plates with the following antibodies and cytokines for pTh17 subset polarizing condition in RPMI-1640 with 10% fetal bovine serum(FBS): 2 μg/ml anti-CD3/CD28, 100 U/ml IL-2, 10 ng/ml IL-6, 10 ng/ml IL-1β, 10 ng/ml IL-23, 5 μg/ml anti-IL-4, 5 μg/ml anti-IFN-γ. The polarized pTh17 subsets were cultured with YY1 shRNA lentivirus (MOI=20), control lentivirus (MOI=20) after cytokines stimulation for 24 h .Cells were grown for 3 days at 37°C in 5% CO2. On day 4, cells were extracted using the standard Trizol method for microarray.

first: Jifeng

last: Tang


title: Transcriptional profiling of the Candida auris response to exogenous farnesol exposure

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: The antifungal resistance threat posed by Candida auris necessitates bold and innovative therapeutic options. Farnesol, a quorum-sensing molecule with a potential antifungal and/or adjuvant effect; it may be a promising candidate in alternative treatment regimens. To gain further insights into the farnesol-related effect on C. auris, genome-wide gene expression analysis was performed using RNA-Seq. Farnesol exposure resulted in 1,766 differentially expressed genes. Of these, 447 and 304 genes with at least 1.5-fold increase or decrease in expression, respectively, were selected for further investigation. Genes involved in morphogenesis, biofilm events (maturation and dispersion), gluconeogenesis, iron metabolism, and regulation of RNA biosynthesis showed down-regulation, whereas those related to antioxidative defense, transmembrane transport, glyoxylate cycle, fatty acid β-oxidation, and peroxisome processes were up-regulated. In addition, farnesol treatment increased the expression of certain efflux pump genes, including MDR1, CDR1, and CDR2. Growth, measured by change in CFU number, was significantly inhibited within 2 hours of the addition of farnesol (5.8×10^7±1.1×10^7 and 1.1×10^7±0.3×10^7 CFU/ml for untreated control and farnesol-exposed cells, respectively) (p<0.001). In addition, farnesol treatment caused a significant reduction in intracellular iron (152.2±21.1 vs. 116.0±10.0 mg/kg), manganese (67.9±5.1 vs. 18.6±1.8 mg/kg), and zinc (787.8±22.2 vs. 245.8±34.4 mg/kg) (p<0.05–0.001) compared to untreated control cells, whereas the level of cooper was significantly increased (274.6±15.7 vs. 828.8±106.4 mg/kg) (p<0.001). Our data demonstrate that farnesol significantly influences the growth, intracellular metal ion contents, and gene expression related to fatty acid metabolism, which could open new directions in developing alternative therapies against C. auris.

overall_design: Examination of untreated control and farnesol-treated Candida auris cultures in three replicates.

first: Renátó

last: Kovács

first: Ágnes


title: Robustness in the feedback control of the retinoic acid network response to environmental disturbances (BioMark-qRT-PCR)

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

summary: Retinoic acid (RA) is a central developmental signal whose perturbation results in teratogenic outcomes. RA is tightly regulated during early embryonic development to achieve fine-tuning of the instructive and permissive signals regulating multiple developmental processes including head formation. We aim to identify the key mechanisms underlying the homeostatic regulation and tuning of the retinoic acid signaling levels, the disruption of which in the head lead to wide ranging developmental malformations including microcephaly and other craniofacial defects. We performed transient physiological RA signaling disturbances during Xenopus laevis embryogenesis followed by kinetic gene expression analysis of the recovery at multiple time points.

overall_design: We considered multiple experimental perturbations including exogenous addition of 10 nM RA, inhibition of RA production by 50 uM DEAB (an inhibitor of RALDH2 enzyme) and no exposure control. We obtained data from six independent clutches for each experimental condition. The embryos were isolated at multiple time points (t=0, 1.5, 3, and 4.5 hours) following two hours of perturbation and a wash.

first: Madhur

last: Parihar

first: Liat

last: Bendelac-Kapon

first: Michal

last: Gur

first: Abha

last: Belorkar

first: Sirisha

last: Achanta

first: Keren

last: Kinberg

first: Abraham

last: Fainsod


title: Identification of downstream molecules associated with TLR4-dependent  inflammatory response in primary bone marrow-derived macrophages (BMDMs) by PolyA-RNA sequencing.

city: Hanghzou

first: Fuye

last: Yang

state: Zhejiang

address: 88 Jiefang Road

department: Nephrology

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

summary: To explore the downstream molecules that are responsible for the regulatory role of macrophage-specific TLR4 during inflammatory responses, we analyzed the transcriptome profile of BMDMs isolated from tlr4f/f and tlr4f/f-lysM-Cre mice with or without LPS stimulation by PolyA RNA sequencing.

overall_design: Primary BMDMs of tlr4f/f and tlr4f/f-lysM-Cre mice were stimulated with 1µg/mL of Lipopolysaccharides (LPS) for 6 hours in vitro. Then, three samples of total mRNAs from each group including control-tlr4f/f, control-tlr4f/f-lysM-cre, LPS-tlr4f/f and LPS-tlr4f/f-lysM-cre were subjected for polyA-RNA sequencing to analyze the effect of macrophage-specific TLR4 on the differential gene expression in response to LPS.

first: Jiaoyi

last: Chen

first: Xiao

last: Huang

first: Wai

last: Yiu

first: Xueqing

last: Yu

first: Sydney

first: Hui

last: Lan


title: Analysis of Oncogenic Cooperation during Leukemia Progression by Single Cell RNA-seq

status: Public on Sep 28 2021

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide determinants of Tn5 insertion preference

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: We generated Tn5 segmentation data on naked genomic DNA to explore the intrinsic Tn5 insertion preference along the whole genome

overall_design: E14 cell line, HSPC primary cell from mouse, and K562 cell line were researched here. To explore the intrinsic Tn5 insertion preference, we extracted naked genomic DNA from these three cell types and used Tn5 for segmentation followed by sequencing. Each cell type has 2 or 3 biological replicates.

first: Ting

last: Lu

first: Houyu

last: Zhang


title: Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [10X]

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

institute: KU Leuven

overall_design: 10X single-cell RNA-seq

first: Irene

last: Talon

first: Adrian

last: Janiszewski

first: Bart

last: Theeuwes

first: Thomas

last: Lefevre

first: Juan

last: Song

first: Greet

last: Bervoets

first: Lotte

last: Vanheer

first: Natalie

last: De Geest

first: Suresh

last: Poovathingal

first: Ryan

last: Allsop

first: Jean-Christophe

last: Marine

first: Florian

last: Rambow

first: Thierry

last: Voet


title: Epigenetic bases of grafting-induced vigour in eggplant

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham


title: Macrophages from Rosa26-integrated Cas9-expressing C57BL/6 mice have a putative TRIF-mediated defect in the TLR-3/4 signaling

status: Public on Sep 27 2021

first: Ang

last: Cui

state: MA

address: 415 Main St.

institute: Broad Institute

summary: In this study, we report that the TLR4 ligand, LPS, and TLR3 ligand polyinosinic:polycytidylic acid failed to activate IRF3 or STAT1 in bone marrow–derived macrophages (BMMs) isolated from two independently generated lines of Rosa26-integrated Cas9-expressing C57BL/6J (B6) mice. RNA-sequencing analysis reveals that hundreds to thousands of genes including IFN-stimulated genes were differentially expressed in BMMs from these Cas9 strains compared with B6 upon LPS stimulation. Furthermore, the NF-kB signaling axis and TRIF-mediated necroptosis were also strongly reduced in response to LPS and polyinosinic:polycytidylic acid. In contrast, there were no defects in the responses of BMMs to ligands of the RIG-I, STING, TLR2, TLR9, and IFN receptors. Defects in TLR3 and TLR4 signaling were observed in mice with the B6 but not 129 background, and when Cas9 was integrated at the Rosa26 but not H11 locus. However, integration at the Rosa26 site, CAG promoter–driven Cas9 or eGFP were not individually sufficient to cause the defect. Taken together, the results of this study suggest a putative TRIF-mediated defect in TLR-3/4 signaling in BMMs from commercially available and widely used B6–Cas9–expressing mice. ImmunoHorizons, 2021, 5: 818–829.

overall_design: RNA-seq analysis of bone marrow derived macrophages derived from wildtype and two Cas9-expressing mice upon stimulation with LPS.

first: Raktima

last: Raychowdhury

first: Matteo

last: Gentili

first: Lawrence

last: Schweitzer

first: Bo

last: Li

first: Nir

last: Hacohen


title: A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

city: Daejeon

first: Hyelim

last: Jo

address: 335 Gwahangno, Yuseong-Gu

department: Biological science

country: South Korea

institute: KAIST

summary: We employed in situ Hi-C with an auxin-inducible degron (AID) system to demonstrate the effect of chromatin remodeling on 3D genome organization in yeast.

overall_design:
IAA (Sigma, I2886) was added to a final concentration of 0.5 mM for degradation of target proteins and the same volume of 100% ethanol was used as a control. For G1 arrest, alpha-factor was added at a final concentration of 50 ng/ml to bar1Δ strains; after 2 h, 0.5 mM IAA was added and the cells were incubated for an additional 3 h. For S or G2/M arrest, alpha-factor was added at a final concentration of 50 ng/ml to bar1Δ strains; after 1.5 h, the yeast cells were transferred to fresh YPD medium containing 200 mM hydroxyurea (HU; Sigma, H8627) for S arrest or 15 ug/ml nocodazole (Sigma, M1404) for G2 arrest. At 1.5 h after HU/nocodazole treatment, 0.5 mM IAA was added and cells were incubated for an additional 3 h. For G2 arrest, an additional 10 ug/ml of nocodazole was applied along with the IAA.
Yeast cells (50 O.D.600) were cultured, fixed with 3% formaldehyde (Wako, 064-00406), quenched, pelleted, pre-incubated with β-ME buffer (20 mM EDTA and 0.7 M β-ME) for 10 min at 30℃, and then lysed with 2 mg of zymolase (US Biological, Z1004) in 2 ml lyticase buffer (1 M sorbitol, 50 mM Tris-Cl (pH 8.0), 5 mM β-ME) for 20 min at 30℃. The obtained spheroplasts were resuspended in 2 ml of ice-cold PBS. The isolated nuclear DNA was resuspended in 50 ul of 0.5% SDS, incubated for 10 min at 62℃, mixed with 170 ul of 1.47% TritonX-100 and incubated for 15 min at 37℃. The generated libraries were sequenced using 150-bp paired-end reads on an Illumina Novaseq6000 and/or HiSeqX.

first: Daeyoup

last: Lee


title: Global transcriptome profiling hnRNP LL depleted 293T cells

city: Kansas City

first: Ning

last: Zhang

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: We performed RNA-seq of 293T cells post depletion of hnRNP LL to look for changes brought about in the transcriptome.

overall_design: For transcriptome analysis, 293T cells were treated with scramble siRNA pool or siRNA targetting hnRNP LL. Cells were treated for 72 hours with the siRNAs before proceeding for RNA extraction.

first: Saikat

last: Bhattacharya

first: Jerry

last: Workman


title: Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies

status: Public on Sep 26 2021

city: Salt Lake City

first: Gabor

last: Marth

state: UT

department: Human Genetics

institute: University of Utah

summary: We collected 42 samples from a breast cancer patients including 28 metastatic tumors (which also had DNA samples) and 14 surrounding normal samples. We generated RNAseq data from these samples to study the differential expression of the metastatic tumors.

overall_design:
RNAseq on 42 sample from the patient’s body at autopsy, including 28 gross tumors and 14 surrounding normal samples.
NOTE FROM SUBMITTER: Raw data (RNAseq reads) consist of identifiable information of human subjects. We are uploading the raw data files to controlled access repository dbGaP.

first: Xiaomeng

last: Huang

first: Yi

last: Qiao

first: Samuel

last: Brady

first: Adam

last: Cohen

first: Andrea

last: Bild


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [aCD3 stimulation]

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Integrative system approaches uncover a three-tier system for the regulatory modules of nutrient signaling-dependent mTORC1 activation in primary T cells

overall_design: We used Microarray to compare gene expression of sgNTC with sgSmarcb1 transduced iTreg

first: Lingyun

last: Long

first: Hao

last: Shi


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [TCR stimulation]

overall_design: We used Microarray to compare gene expression of sgNTC with sgCcdc101 transduced iTreg after TCR restimulation


title: Robustness of retinoic acid regulatory homeostasis during early development (RNA-seq)

first: Rajanikanth

last: Vadigepalli

summary: Retinoic acid (RA) is a central developmental signal whose perturbation results in teratogenic outcomes. RA are tightly regulated during early embryonic development to achieve fine-tuning of the instructive and permissive signals regulating multiple developmental processes including head formation. We aim to identify the key mechanisms underlying the homeostatic regulation and tuning of the retinoic acid signaling levels, the disruption of which in the head lead to wide ranging developmental malformations including microcephaly and other craniofacial defects. We performed transient physiological RA signaling disturbances during Xenopus laevis embryogenesis followed by kinetic RNAseq analysis of the recovery at multiple time points.

overall_design: We considered multiple experimental perturbations including exogenous addition of 10 nM RA, inhibition of RA production by 50 uM DEAB (an inhibitor of RALDH2 enzyme), 0.5% ethanol exposure, and no exposure control. We obtained data from six independent clutches for each experimental condition. The embryos were isolated at multiple time points (t=0, 1.5, 3, and 4.5 hours) following two hours of perturbation and a wash.

first: Madhur

last: Parihar

first: Liat

last: Bendelac-Kapon

first: Michal

last: Gur

first: Abha

last: Belorkar

first: Keren

last: Kinberg

first: Abraham

last: Fainsod


title: RNA-seq analysis of transcriptomic changes in control (shLuc) and GEM knockdown (shGem) bone marrow LSK cells

first: Jian

last: Xu

summary: Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employed single-cell RNA sequencing to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid expansion with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically control gene expression in single cells. We integrated results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We used this resource to relate developmental hierarchies to leukemia phenotypes, evaluated oncogenic cooperation at single-cell and single-gene levels, and identified GEM as a new regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution in vivo.

overall_design: Lineage negative cells were transduced with shRNA virus against luciferase (shLuc) or GEM (shGem). Positively transduced cells (GFP+) were sorted by FACS 72 hours post-transduction and subjected to RNA-seq library preparation. RNA-seq library was prepared using the SMARTer stranded pico input total RNA-seq kit (Takara)

first: Yuxuan

last: Liu

first: Zhimin

last: Gu


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [scRNA-seq]

summary: Integrative system approaches uncover a three-tier system for the regulatory modules of nutrient signaling-dependent mTORC1 activation in regulatory T cells

overall_design: We used scRNA-seq to profile CD45+YFP+ Treg cells, CD45+YFP-CD11b- non-Treg cells and CD45+CD11b+ myeloid cells (mixed at 1:2:1 ratio) in the MC38 colon adenocarcinoma


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [sgCcdc101 ATAC-seq]

overall_design: We used ATAC-seq to compare chromatin accessibility profiles of sgCcdc101 and sgNTC transduced iTreg cells

first: Jun

last: Wei


title: Asymmetric robustness in the feedback control of the retinoic acid network response to environmental disturbances


title: G3BP1 inhibits Cul3SPOP to amplify AR signaling and promote prostate tumorigenesis

city: New York

first: Deli

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Speckle-type POZ protein (SPOP), an E3 ubiquitin ligase, acts as a tumor suppressor. We identified G3BP1 as non-substrate interactor of SPOP. G3BP1 is a well-known oncogene in many cancer types, but its role in prostate cancer (PCa) remains largely elusive. We showed that G3BP1 functions as an upstream regulator and potent endogenous inhibitor of Cul3SPOP, suggesting a distinctive Cul3SPOP inactivation independent of SPOP mutations. Transcriptomic analysis together with functional studies revealed that the G3BP1-SPOP ubiquitin signaling axis is involved in PCa progression through activating AR signaling. Further, AR upregulates G3BP1 to potentiate feed-forward amplification of signaling through G3BP1-SPOP axis. Overall, we show G3BP1high PCa tumors constitute a new subset where G3BP1 inhibits Cul3SPOP function to upregulate AR signaling, and promotes tumorigenesis.

overall_design: Differentially expressed genes between loss of G3BP1 vs ctrl and knockdown of SPOP vs ctrl

first: Chandrani

last: Mukhopadhyay

first: Pengbo

last: Zhou


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [steady state]

first: Hongbo

overall_design: We used Microarray to compare gene expression of sgNTC with sgCcdc101 transduced iTreg at steady state


title: Expansion of Human Papillomavirus-Specific T Cells in Periphery and Cervix in a Therapeutic Vaccine Recipient Whose Cervical High-Grade Squamous Intraepithelial Lesion Regressed

status: Public on Sep 25 2021

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

summary: Single-cell TCR/transcriptome analysis for a peripheral blood lymphocytes (PBL) specimen was perform on a 10X Chromium instrument using a single-cell VDJ kit

overall_design: Single-cell TCR/transcriptome analysis was performed on a PBL specimen, obtained from a patient who received a thrapeutic HPV vaccine. For details, please read the manuscript, which has been accepted for publication in the journal Frontiers in Immunology.

first: Mayumi

last: Nakagawa


title: PI3Kd coordinates transcriptional, epigenetic and metabolic changes to promote effector CD8+ T cells differentiation at the expense of memory.

city: Bethesda

first: Han-Yu

last: Shih

state: MD

address: 10 Center Drive Rm 5S261

institute: National Eye Institute

summary: Patients with Activated-PI3Kd Syndrome (APDS) present with sinopulmonary infections, lymphadenopathy and CMV and/or EBV viremia, yet why patients fail to clear certain viral infections remains incompletely understood. Using patient samples and a mouse model (Pik3cdE1020K/+ mice), we demonstrate that, upon activation, Pik3cdE1020K/+ CD8+ T cells exhibit exaggerated features of short-lived effectors both in vitro and post-viral infection, including increased Fas-mediated apoptosis due to sustained FoxO1 phosphorylation and derepression of FasL. Activated Pik3cdE1020K/+ CD8+ T cells displayed enhanced mTORC1 and c-Myc signatures, accompanied by metabolic perturbations linked to an accelerated effector program. Conversely, Pik3cdE1020K/+ CD8+ T cells failed to sustain expression of proteins critical for maintenance of long-lived memory cells, including TCF1, and mounted inadequate memory responses in vivo. Strikingly, activated Pik3cdE1020K/+ CD8+ T cells exhibit altered transcriptional and epigenetic circuits characterized by a pronounced IL-2/STAT5 signature associated with heightened IL-2 responses that prevented differentiation to memory-like cells in the presence of IL-15. Our data position PI3Kd as a central hub integrating multiple signaling nodes that promote terminal CD8+ T cell effector differentiation at the expense of memory and long-lived T cell responses.

overall_design: Integrated analysis of RNA-seq and ATAC-seq data from Wild-type and Pik3cdE1020K/+ CD8+ cells.

first: J

middle: L

last: Cannons

first: A

middle: V

last: Villarino

first: S

last: Kapnick S

last: Preite

first: H-Y

last: Gomez-Rodriguez

last: Reilley

first: B

last: Huang

first: R

last: Handon

first: I

last: McBain

first: T

last: Wu

first: H

last: Su H

first: D

last: McGavern

middle: J

last: O'Shea

first: P

last: McGuire

first: G

last: Uzel

last: Schwartzberg


title: Single cell RNA-seq analysis of transcriptomics in WT and E2-KO, G12D and G12D/E2-KO HSPCs from mouse bone marrow

first: Jian

last: Xu

summary: Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employ single-cell RNA sequencing to map cellular composition and gene expression alterations in healthy or diseased bone marrows underlying leukemia progression. At cellular levels, while NRasG12D induces myeloid-biased differentiation and EZH2-deficiency impairs myeloid maturation, they cooperate to promote myeloid expansion with dysregulated transcriptional programs. At gene levels, NRasG12D and EZH2-deficiency independently or synergistically control gene expression in single cells. We integrate results from histopathology, flow cytometry, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We use this resource to relate developmental hierarchies to leukemia phenotypes, evaluate oncogenic cooperation at single-cell levels, and identify new regulators of leukemia-initiating cells. Our studies establish an integrative approach to capture the kinetics of cancer evolution in vivo.

overall_design: Single cell RNA-seq was performed to determine the cell identity and transcriptomic changes in WT E2-KO, G12D and G12D/E2-KO HSPCs from mouse bone marrow.

first: Yuxuan

last: Liu

first: Zhimin

last: Gu


title: Progenitor Translatome Changes Coordinated by Tsc1 Increase Perception of Wnt Signals to End Nephrogenesis

status: Public on Sep 24 2021

city: Cincinnati

first: Alison

last: Jarmas

state: Ohio

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

overall_design: Refer to individual Series


title: Progenitor Translatome Changes Coordinated by Tsc1 Increase Perception of Wnt Signals to End Nephrogenesis  [10x_scRNA-seq]

summary: This series contains scRNA-Seq data generated using the 10x Genomcis chromium v2 platform for embryonic day 14 and postnatal day 0 mouse kidneys isolated from three different genotypes representing control and elevated nephron number mouse phenotypes.

overall_design: Evaluation of single cell transcriptomic singaturers of cells isolated from the developing mouse kidney cortex

first: Eric

last: Brunskill

first: Praneet

last: Chaturvedi

first: Raphael

last: Kopan


title: Transcriptomic analysis of Drosophila larval and adult blood cells

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary: Drosophila adult blood cells originate from larval peripheral hemocytes (derived from the embryonic waves of hematopoiesis) and from larval lymph gland hemocytes. To gain insight into the expression repertoire of Drosophila blood cells, we established the gene expression profiles the adult blood cells and their ascendants.

overall_design: We used Drosophila melanogaster w1118 females to retrieve total blood cell populations. Adult blood cells were collected by bleeding 5-day old flies;  3rd instar larval hemocytes were retrieved by bleeding (for embryo-derived hemocytes) or by dissecting the anterior lobes of the lymph glands.Total RNAs were extracted for analysis by deep sequencing, in triplicate, using Illumina NextSeq sequencing platform.

first: Lucas

last: Waltzer

first: Yoan

last: Renaud


title: Next Generation Sequencing Facilitates Quantitative Analysis of sorted lymphatic endothelial cells from the murine skin at 4 different time points of the day: ZT1, ZT7, ZT13, ZT19

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare adhesion gene clusters and clock genes / biomarkers at different time points throughout the day in sorted murine lympahtic endothelial cells.
Methods: RNA of sorted dermal LECs harvested in TriZol-LS was purified using Direct-zol RNA mini Prep Kit (ZymoResearch) following manufacturer’s instructions. Isolated RNA was quantified using the Nanodrop (Thermofisher) and analyzed on a Bioanalyzer (Agilent) using the RNA 6000 Nano or Pico Kit (Agilent). 75 ng of eluted total RNA was digested with DNase (Thermofisher) to remove DNA contaminations. An additional purification step with RNAClean XP Beads (Agencourt) was performed. The purified, bead-bound RNA was directly used as input in the SMART-Seq v4 Ultra Low Input RNA Kit (TaKaRA Bio). Full-length cDNA was generated following manufacturer’s instructions. Full-length cDNA was quantified using the Qubit dsDNA HS Assay Kit (Invitrogen) with the Qubit fluorometer. Finally, sequencing libraries were generated using 500 pg full-length cDNA following the NexteraXT protocol (Illumina). Libraries were quantified on a Bioanalyzer (Agilent) using the DNA 1000 Kit (Agilent) and sequenced on a HiSeq1500 system (Illumina) with a readlength of 100 nt, single-end mode.
Results: obtained transcriptome profiles were processed on a Galaxy web interface hosted by LAFUGA (Gene Center, Munich). After demultiplexing and trimming data was mapped against the mouse genome (mm10) using RNA-STAR mapper (Galaxy Version 2.5.2b-0). Abundant reads were counted using HTSeq-count (Galaxy Version 1.0.0). Afterwards, gene expression analysis to detect differentially expressed genes was performed using DESeq2 (Galaxy Version 2.11.40.6), setting the false discovery rate (FDR) <0.05. Comparing the expression profiles and the enrichment of gene ontology cluster adhesion revealed a highly time-of-day dependent expression profile of genes.
Conclusions: Our study represents the first detailed analysis of time-of-day dependent lymphatic endothelial cell transcriptomes, with respect to adhesion and clock genes. This will provide valid input into chronotherapy, timed delivery of substances and new therapeutic avenues.

overall_design: 5 mRNA samples of four time points each from mouse skin were sequenced on a HiSeq1500 system (Illumina) with a readlength of 100 nt, single-end mode.

first: Julia

last: Philippou-Massier


summary: This series contains bulk RNA-Seq data dervied from FACS-isolated nephron progenitor cells for transcripts associated with ribosomal protein L10a (TRAP approach)

overall_design: Evaluation of the ribosomal-protein L10a associated transcript signature of nephron progenitor cells isolated from embryonic day 14 or postnatal day 0 control strain mice, or P0 Tsc1+/- nephron progenitor cells associated with increased nephron number.


title: Overcoming GNA/RNA Base-Pairing Limitations Using Isonucleotides Improves the Pharmacodynamic Activity of ESC+ GalNAc-siRNAs

city: Cambridge

first: Joseph

last: Barry

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

summary: We report the impact of two pairs of GNA nucleotides, the native GNA-C and -G compared with the isomeric GNA-isoC and -isoG, on the on- and off-target activity of chemically modified siRNAs in primary mouse hepatocytes by RNA sequencing.  We found that both GNA-C and -isoC mitigate the suppression of off-targets in a similar fashion, however, GNA-isoG was less efficacious in the mitigation of off-targets as the native GNA-G.  This study informs the further design of more potent and specific chemically modified siRNAs for potential application in RNAi therapeutics.

overall_design: This experiment intended to compare the specificity of several different chemicallly modified siRNAs after transfection into primary mouse hepatocytes and was aimed at demonstrating the similarities or differences between two pairs of chemically modified nucleotides when incorporated into the same position of an identical siRNA sequence.

first: Mark

middle: K

last: Schlegel

first: Shigeo

last: Matsuda

first: Christopher

last: Brown

first: Joel

last: Harp

first: Daniel

last: Berman

first: Adam

last: Castoreno

first: Sally

last: Schofield

first: John

last: Szeto

first: Muthiah

last: Manoharan

first: Klaus

last: Charisse

first: Martin

last: Egli

middle: A

last: Maier


title: Transcriptomics reveals the mycoparasitic strategy of the mushroom Entoloma abortivum on species of the mushroom Armillaria

status: Public on Sep 23 2021

city: Lincoln

first: Rachel

middle: Anne

last: Koch

state: NE

address: 1875 N 38th Street

department: Plant Pathology

institute: University of Nebraska

summary: During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in Ascomycete fungi. However, within Basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially expressed E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most significantly upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species, however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome were reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction.

sample_organism:
Armillaria mellea
Entoloma abortivum

platform_organism:
Armillaria mellea
Entoloma abortivum

overall_design: Field-collected sporocarps (fruiting bodies) for each species in this interaction--Entoloma abortivum and Armillaria mellea--were sequenced. For each species, three biological replicates of individual sporocarps were sequenced and three technical replicates of each of those biological replicates were also sequenced. Sporocarps were considered "baseline" treatments. Then for the mixed tissue, or carpophoroids, which contain both E. abortivum and A. mellea, three biological replicates were also sequenced, along with three technical replicates for each biological replicate. Gene expression for each species was analyzed as to how it differed between the sporocarps and carpophoroids.

first: Joshua

last: Herr


title: Arthritis Flares Mediated by Tissue Resident Memory T Cells in the Joint

city: Newton

first: Margaret

last: Chang

address: 300 Longwood Ave, Fegan 6

institute: Boston Children's Hospital

summary: Rheumatoid arthritis is a systemic autoimmune disease, but disease flares typically affect only a subset of joints, distributed in a pattern that is distinctive for each patient. Pursuing this intriguing pattern, we show that arthritis recurrence is mediated by long-lived synovial resident memory T cells (TRM). In three murine models, CD8+ cells bearing TRM markers remain in previously inflamed joints during remission. These cells are bona fide TRM, exhibiting failure to migrate from joint to joint, preferential uptake of fatty acids, and long-term residency. Disease flares result from TRM activation by antigen, leading to CCL5-mediated recruitment of circulating effector cells. Correspondingly, TRM depletion ameliorates recurrence in a site-specific manner. Human rheumatoid arthritis joint tissues contain a comparable CD8+-predominant TRM population, most evident in late-stage leukocyte-poor synovium, exhibiting limited T cell receptor diversity and a pro-inflammatory transcriptomic signature. Together, these findings establish synovial TRM cells as a targetable mediator of disease chronicity in autoimmune arthritis.

overall_design:
Memory T cells isolated and pooled from 5 human RA synovium donors, subjected to single-cell RNA sequencing
**Raw data not available due to patient privacy concerns**

first: Anaïs

last: Levescot

first: Nathan

last: Nelson-Maney

middle: B

last: Blaustein

first: Kellen

middle: D

last: Winden

first: Allyn

last: Morris

first: Alexandra

last: Wactor

first: Spoorthi

last: Balu

first: Ricardo

last: Grieshaber-Bouyer

first: Kevin

last: Wei

first: Lauren

last: Henderson

first: Yoichiro

last: Iwakura

first: Rachael

last: Clark

first: Deepak

last: Rao

first: Robert

last: Fuhlbrigge

first: Peter

last: Nigrovic